Hi,

Have been tried that but still exited with errors. is it because of iMac doesn't enable freesurfer to create the subject files without security password? do anybody know how to settle this problems?

Thank you.

Best, Isma

________________________________ From: Jürgen Hänggi j.haenggi@psychologie.uzh.ch To: aini ismafairus aini_ismafairus@yahoo.com.my; Freesurfer Mailinglist freesurfer@nmr.mgh.harvard.edu Sent: Saturday, 1 December 2012 12:42 PM Subject: Re: [Freesurfer] recon-all error

Re: [Freesurfer] recon-all error Dear Aina

Unzip us03.nii.gz and try it again

Cheers Jürgen

On [DATE], "aini ismafairus" <[ADDRESS]> wrote:

Hello,

I still new in using freesurfer. the freesurfer was successfully installed. but when i tried to run recon-all it give an error.

[Ainis-iMac:~] ismafairus% setenv FREESURFER_HOME Applications/freesurfer [Ainis-iMac:~] ismafairus% source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   Applications/freesurfer FSFAST_HOME       Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      Applications/freesurfer/subjects MNI_DIR           Applications/freesurfer/mni FSL_DIR           FSL/fsl

Ainis-iMac:~] ismafairus% recon-all -i $SUBJECTS_DIR/us03.nii.gz -o us03 -all ERROR: cannot find Applications/freesurfer/subjects/us03.nii.gz Darwin Ainis-iMac.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64

recon-all -s  exited with ERRORS at Sat Dec  1 11:42:54 CET 2012

Advice on how to troubleshoot this would be appreciate.

Thank you.

Regards, Isma

...

---

---

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---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile)        0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number)                      j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)

This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

what happens if you do

ls -l $SUBJECTS_DIR/us03.nii.gz

and

mri_info $SUBJECTS_DIR/us03.nii.gz

On Sun, 2 Dec 2012, aini ismafairus wrote:

Hi,

Have been tried that but still exited with errors. is it because of iMac doesn't enable freesurfer to create the subject files without security password? do anybody know how to settle this problems?

Thank you.

Best, Isma

---

From: Jürgen Hänggi j.haenggi@psychologie.uzh.ch To: aini ismafairus aini_ismafairus@yahoo.com.my; Freesurfer Mailinglist freesurfer@nmr.mgh.harvard.edu Sent: Saturday, 1 December 2012 12:42 PM Subject: Re: [Freesurfer] recon-all error

Dear Aina

Unzip us03.nii.gz and try it again

Cheers Jürgen

On [DATE], "aini ismafairus" <[ADDRESS]> wrote:

  Hello,

  I still new in using freesurfer.
  the freesurfer was successfully installed.
  but when i tried to run recon-all it give an error.


  [Ainis-iMac:~] ismafairus% setenv FREESURFER_HOME
  Applications/freesurfer
  [Ainis-iMac:~] ismafairus% source
  $FREESURFER_HOME/SetUpFreeSurfer.csh
  -------- freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
  --------
  Setting up environment for FreeSurfer/FS-FAST (and FSL)
  FREESURFER_HOME   Applications/freesurfer
  FSFAST_HOME       Applications/freesurfer/fsfast
  FSF_OUTPUT_FORMAT nii.gz
  SUBJECTS_DIR      Applications/freesurfer/subjects
  MNI_DIR           Applications/freesurfer/mni
  FSL_DIR           FSL/fsl

  Ainis-iMac:~] ismafairus% recon-all -i $SUBJECTS_DIR/us03.nii.gz
  -o us03 -all
  ERROR: cannot find Applications/freesurfer/subjects/us03.nii.gz
  Darwin Ainis-iMac.local 12.2.1 Darwin Kernel Version 12.2.1: Thu
  Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64
  x86_64

  recon-all -s  exited with ERRORS at Sat Dec  1 11:42:54 CET 2012


  Advice on how to troubleshoot this would be appreciate.

  Thank you.

  Regards,
  Isma

---

  _______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


  The information in this e-mail is intended only for the person
  to whom it is
  addressed. If you believe this e-mail was sent to you in error
  and the e-mail
  contains patient information, please contact the Partners
  Compliance HelpLine at
  http://www.partners.org/complianceline . If the e-mail was sent
  to you in error
  but does not contain patient information, please contact the
  sender and properly
  dispose of the e-mail.

---

Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile)        0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number)                      j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)

This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden.

---

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.